Implement sample merging - #1026

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Donaim wants to merge 11 commits into

Commits on Feb 14, 2024

Make bad_cycles.csv argument optional in trim_fastqs.py
Donaim
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6184dc2
Add merge_samples command to micall_docker.py
Donaim
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e69c5f2
Factor merge_fastqs from micall_docker.py into a separate script
Donaim
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de0ba91
Add Singularity entry for the new merge_fastqs pipeline
Donaim
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899f480
Fix input arguments to merge_fastqs in Singularity file
Donaim
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10f8350
Add more tests for merge_fastqs.py script
Donaim
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26cc823
Ensure that output directories exist in merge_fastqs.py
Donaim
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8e00a51
Fix typo in merge_fastqs.py
Donaim
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df9b3b6
Compress final outputs in merge_samples when --unzip is not used
Donaim
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6840f80

Commits on Feb 16, 2024

Merge fastqs: support arbitrary number of inputs
Donaim
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0020301
Merge fastqs: add documentation
Donaim
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d09fc56